Matthew Schechter of anvi'o

Bio

Microbiologist interested in combining comparative genomics and environmental metagenomics to identify genetic determinants of fitness in microbial populations in the human gut and ocean microbiome.

Affiliations

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Program contributions

anvi-analyze-synteny anvi-export-locus anvi-run-hmms anvi-run-workflow anvi-script-filter-hmm-hits-table

Resource contributions

Tutorials and exercises

Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.

A metagenomics workshop featuring anvi'o Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
metagenomics metabolism hands-on beginner

Technical write-ups

Solutions or discussions regarding matters that are typically more technical than scientific.

Extract loci from genomes and metagenomes with anvi'o A tutorial on how to use anvi-export-locus to target genomic regions of interest across genomes and/or metagenomic assemblies, and report sequences and/or anvi’o contigs databases for cut loci for downstream analyses.
genomics hands-on intermediate
Integrating AGNOSTOS gene categories into anvi'o projects A workflow to demonstrate how to import AGNOSTOS gene categories into anvi'o databases
metagenomics pangenomics hands-on advanced

Articles, workflows, opinions

Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.

The history of metagenomics: An incomplete summary An incomplete history of ideas that shpaped integrated genomics and metagenomics to explore microbial fitness in habitats such as the human gut and the oceans.
metagenomics beginner